scPDB - 4ax8 entry

Protein Data Bank Entry:

PDB ID : 4ax8

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2012-06-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	O-antigen chain terminator bifunctional methyltransferase/kinase WbdD
ID:	WBDD_ECOLX
AC:	J7I4B7
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	58.465
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.561	590.625

% Hydrophobic	% Polar
50.86	49.14
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	73.2 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
48.5059	65.2074	92.1681

Binding mode :

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
SD	CZ	TYR- 16	4.21	0	Hydrophobic	false
CE	CE1	TYR- 16	3.63	0	Hydrophobic	false
CG	CE2	TYR- 16	3.66	0	Hydrophobic	false
OXT	NE2	GLN- 17	2.88	162.23	H-Bond (Protein Donor)	false
O	NH1	ARG- 36	2.84	175.13	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 36	3.18	149.54	H-Bond (Protein Donor)	false
O	CZ	ARG- 36	3.71	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 36	3.85	0	Ionic (Protein Cationic)	false
N	O	GLY- 61	2.85	155.92	H-Bond (Ligand Donor)	false
CB	CB	ALA- 63	3.64	0	Hydrophobic	false
O2'	OD1	ASP- 82	2.54	147.42	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 82	3.28	147.9	H-Bond (Ligand Donor)	false
N3	N	PHE- 83	3.2	139.16	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 83	3.95	0	Aromatic Face/Face	false
C2'	CE1	PHE- 83	3.97	0	Hydrophobic	false
O2'	NE2	GLN- 84	2.95	156.6	H-Bond (Protein Donor)	false
N1	N	ILE- 110	2.92	161.07	H-Bond (Protein Donor)	false
N6	OE1	GLU- 111	3.1	165.41	H-Bond (Ligand Donor)	false
N	O	LEU- 128	2.73	156.67	H-Bond (Ligand Donor)	false
CG	CB	SER- 129	4.3	0	Hydrophobic	false